Loading report..

Highlight Samples

Regex mode off

    Rename Samples

    Click here for bulk input.

    Paste two columns of a tab-delimited table here (eg. from Excel).

    First column should be the old name, second column the new name.

    Regex mode off

      Show / Hide Samples

      Regex mode off

        Export Plots

        px
        px
        X

        Download the raw data used to create the plots in this report below:

        Note that additional data was saved in multiqc_data when this report was generated.


        Choose Plots

        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        Save Settings

        You can save the toolbox settings for this report to the browser.


        Load Settings

        Choose a saved report profile from the dropdown box below:

        Tool Citations

        Please remember to cite the tools that you use in your analysis.

        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.25.2

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2024-12-13, 00:42 CET based on data in: /home/oscar/Desktop/BioinformaticProjects/UpDownRegulated/Project/data/html/Filtered_Alignment


        General Statistics

        Showing 0/18 rows and 5/8 columns.
        Sample NameError rateNon-primaryReads mapped% Mapped% Proper pairs% MapQ 0 readsTotal seqsMean insert
        SRR6984609_trimmed_sorted_quality
        0.25%
        5.5M
        22.3M
        100.0%
        0.0%
        1.8%
        22.3M
        0.0bp
        SRR6984610_trimmed_sorted_quality
        0.21%
        6.7M
        24.6M
        100.0%
        0.0%
        1.7%
        24.6M
        0.0bp
        SRR6984611_trimmed_sorted_quality
        0.18%
        5.9M
        25.6M
        100.0%
        0.0%
        1.2%
        25.6M
        0.0bp
        SRR6984612_trimmed_sorted_quality
        0.12%
        5.1M
        24.4M
        100.0%
        0.0%
        0.7%
        24.4M
        0.0bp
        SRR6984613_trimmed_sorted_quality
        0.21%
        5.8M
        23.9M
        100.0%
        0.0%
        1.5%
        23.9M
        0.0bp
        SRR6984614_trimmed_sorted_quality
        0.11%
        5.2M
        25.9M
        100.0%
        0.0%
        0.7%
        25.9M
        0.0bp
        SRR6984615_trimmed_sorted_quality
        0.24%
        6.3M
        25.1M
        100.0%
        0.0%
        1.8%
        25.1M
        0.0bp
        SRR6984616_trimmed_sorted_quality
        0.15%
        6.8M
        33.3M
        100.0%
        0.0%
        1.0%
        33.3M
        0.0bp
        SRR6984617_trimmed_sorted_quality
        0.14%
        6.1M
        27.9M
        100.0%
        0.0%
        1.0%
        27.9M
        0.0bp
        SRR6984618_trimmed_sorted_quality
        0.13%
        6.1M
        23.0M
        100.0%
        0.0%
        1.0%
        23.0M
        0.0bp
        SRR6984619_trimmed_sorted_quality
        0.16%
        7.0M
        23.4M
        100.0%
        0.0%
        1.4%
        23.4M
        0.0bp
        SRR6984620_trimmed_sorted_quality
        0.14%
        5.6M
        23.3M
        100.0%
        0.0%
        1.1%
        23.3M
        0.0bp
        SRR6984621_trimmed_sorted_quality
        0.32%
        5.7M
        21.9M
        100.0%
        0.0%
        2.4%
        21.9M
        0.0bp
        SRR6984622_trimmed_sorted_quality
        0.19%
        5.3M
        26.8M
        100.0%
        0.0%
        1.1%
        26.8M
        0.0bp
        SRR6984623_trimmed_sorted_quality
        0.25%
        8.6M
        32.2M
        100.0%
        0.0%
        2.0%
        32.2M
        0.0bp
        SRR6984624_trimmed_sorted_quality
        0.17%
        7.0M
        29.8M
        100.0%
        0.0%
        1.1%
        29.8M
        0.0bp
        SRR6984625_trimmed_sorted_quality
        0.18%
        5.5M
        22.9M
        100.0%
        0.0%
        1.3%
        22.9M
        0.0bp
        SRR6984626_trimmed_sorted_quality
        0.12%
        5.4M
        23.9M
        100.0%
        0.0%
        0.9%
        23.9M
        0.0bp

        Samtools

        Version: 1.13

        Toolkit for interacting with BAM/CRAM files.URL: http://www.htslib.orgDOI: 10.1093/bioinformatics/btp352

        Percent mapped

        Alignment metrics from samtools stats; mapped vs. unmapped reads vs. reads mapped with MQ0.

        For a set of samples that have come from the same multiplexed library, similar numbers of reads for each sample are expected. Large differences in numbers might indicate issues during the library preparation process. Whilst large differences in read numbers may be controlled for in downstream processings (e.g. read count normalisation), you may wish to consider whether the read depths achieved have fallen below recommended levels depending on the applications.

        Low alignment rates could indicate contamination of samples (e.g. adapter sequences), low sequencing quality or other artefacts. These can be further investigated in the sequence level QC (e.g. from FastQC).

        Reads mapped with MQ0 often indicate that the reads are ambiguously mapped to multiple locations in the reference sequence. This can be due to repetitive regions in the genome, the presence of alternative contigs in the reference, or due to reads that are too short to be uniquely mapped. These reads are often filtered out in downstream analyses.

        Created with MultiQC

        Alignment stats

        This module parses the output from samtools stats. All numbers in millions.

        Created with MultiQC

        Software Versions

        Software Versions lists versions of software tools extracted from file contents.

        SoftwareVersion
        Samtools1.13